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Model refactor #280

Merged
merged 58 commits into from
May 20, 2024
Merged

Model refactor #280

merged 58 commits into from
May 20, 2024

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HadleyKing
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Refactoring the models in the BCODB for improved maintainability.

HadleyKing and others added 8 commits March 7, 2024 09:15
Changes to be committed:
	modified:   .gitignore
	deleted:    bcodb/settings.py
	renamed:    bcodb/__init__.py -> config/__init__.py
	renamed:    bcodb/asgi.py -> config/asgi.py
	renamed:    bcodb/fixtures/local_data.json -> config/fixtures/local_data.json
	renamed:    bcodb/fixtures/test_portal.json -> config/fixtures/test_portal.json
	renamed:    bcodb/urls.py -> config/urls.py
	renamed:    bcodb/wsgi.py -> config/wsgi.py
	modified:   manage.py
changed model behind `/api/accounts/new/`
Changes to be committed:
	modified:   api/admin.py
	new file:   api/migrations/0006_delete_new_users.py
	modified:   api/models.py
	deleted:    api/scripts/method_specific/POST_api_accounts_new.py
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/admin.py
	modified:   authentication/apis.py
	new file:   authentication/migrations/0002_newuser.py
	modified:   authentication/models.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   tests/fixtures/test_data.json
	modified:   tests/test_views/test_api_account_activate.py
	modified:   tests/test_views/test_api_account_new.py
Changes to be committed:
	modified:   authentication/apis.py
	new file:   docs/refactor.md
On branch account_authorization
Changes to be committed:
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/apis.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   authentication/urls.py
* Account activation has been enabled.

On branch account_authorization
Changes to be committed:
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/apis.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   authentication/urls.py

* get_new_user
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json
Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py
Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py
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gitguardian bot commented Mar 14, 2024

⚠️ GitGuardian has uncovered 10 secrets following the scan of your pull request.

Please consider investigating the findings and remediating the incidents. Failure to do so may lead to compromising the associated services or software components.

🔎 Detected hardcoded secrets in your pull request
GitGuardian id GitGuardian status Secret Commit Filename
4444555 Triggered Django Secret Key 0c0108d config/settings.py View secret
4444555 Triggered Django Secret Key 47d9ed8 bcodb/settings.py View secret
4444555 Triggered Django Secret Key 62142d1 config/settings.py View secret
10002004 Triggered Generic Password 6dd83e6 test.json View secret
10002004 Triggered Generic Password 6366b0b test.json View secret
10002004 Triggered Generic Password 30ba550 test.json View secret
4444557 Triggered Generic High Entropy Secret 02d452f authentication/apis.py View secret
4444557 Triggered Generic High Entropy Secret b3abd90 authentication/apis.py View secret
4444557 Triggered Generic High Entropy Secret 02d452f api/views.py View secret
4444564 Triggered Generic High Entropy Secret d52be01 authentication/services.py View secret
🛠 Guidelines to remediate hardcoded secrets
  1. Understand the implications of revoking this secret by investigating where it is used in your code.
  2. Replace and store your secrets safely. Learn here the best practices.
  3. Revoke and rotate these secrets.
  4. If possible, rewrite git history. Rewriting git history is not a trivial act. You might completely break other contributing developers' workflow and you risk accidentally deleting legitimate data.

To avoid such incidents in the future consider


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HadleyKing and others added 21 commits March 14, 2024 12:16
Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json
* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Move Swagger files and implement BCO draft create

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	new file:   config/services.py
	modified:   config/urls.py
	modified:   docs/refactor.md
	modified:   prefix/urls.py
	new file:   tests/fixtures/example_bco.py
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Doc fix in Bco.models
Changes to be committed:
	modified:   biocompute/models.py
* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Move Swagger files and implement BCO draft create

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	new file:   config/services.py
	modified:   config/urls.py
	modified:   docs/refactor.md
	modified:   prefix/urls.py
	new file:   tests/fixtures/example_bco.py
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Doc fix in Bco.models
Changes to be committed:
	modified:   biocompute/models.py

* Updated biocompute.model and prefix.model

Added the DraftsCreateApi and tests.
This included serializers for BCO creation
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/services.py
	modified:   prefix/models.py
	modified:   prefix/services.py
	modified:   test.json
	modified:   tests/fixtures/test_data.json
	new file:   tests/test_views/test_api_objects_drafts_create.py
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/apis.py
	modified:   prefix/services.py
	modified:   prefix/urls.py
	modified:   search/apis.py
	modified:   tests/test_views/test_api_auth_remove.py
	modified:   tests/test_views/test_api_objects_drafts_create.py
	new file:   tests/test_views/test_api_prefixes_create.py
Changes to be committed:
	modified:   config/fixtures/local_data.json
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/services.py
	modified:   prefix/urls.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_views/test_api_prefixes_create.py
	new file:   tests/test_views/test_prefixes_create.py
	new file:   tests/test_views/test_prefixes_modify.py
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/migrations/0001_initial.py
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	new file:   tests/test_views/test_account_activate.py
	new file:   tests/test_views/test_account_describe.py
	new file:   tests/test_views/test_account_new.py
	new file:   tests/test_views/test_auth_add.py
	new file:   tests/test_views/test_auth_remove.py
	new file:   tests/test_views/test_auth_reset_token.py
	new file:   tests/test_views/test_objects_drafts_create.py
Changes to be committed:
	modified:   authentication/services.py
	modified:   biocompute/models.py
	modified:   config/settings.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/models.py
	modified:   prefix/services.py
	modified:   tests/test_views/test_api_objects_drafts_create.py
On branch prefix_perms
Your branch is up to date with 'origin/prefix_perms'.

Changes to be committed:
	modified:   config/services.py
	modified:   prefix/apis.py
	modified:   prefix/models.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json
Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py
To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json
Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py
Changes to be committed:
	modified:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	modified:   prefix/services.py
	new file:   tests/fixtures/bco_dump.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_add.py
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_apis/test_auth_add.py -> tests/test_apis/test_api_authentication/test_auth_add.py
	renamed:    tests/test_apis/test_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_auth_reset_token.py
	renamed:    tests/test_apis/test_api_authentication/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/testi_auth_remove.py
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	new file:   tests/test_apis/test_api_prefix/__init__.py
	renamed:    tests/test_apis/test_prefixes_create.py -> tests/test_apis/test_api_prefix/test_prefixes_create.py
	renamed:    tests/test_apis/test_prefixes_modify.py -> tests/test_apis/test_api_prefix/test_prefixes_modify.py
	deleted:    tests/test_apis/test_auth_remove.py
	new file:   tests/test_apis/test_biocompute/__init__.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/test_objects_drafts_create.py
* Add `DraftRetrieveApi`

To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json

* Update testing functions

Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py

* Update to Test functions

Changes to be committed:
	modified:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	modified:   prefix/services.py
	new file:   tests/fixtures/bco_dump.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_add.py
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_apis/test_auth_add.py -> tests/test_apis/test_api_authentication/test_auth_add.py
	renamed:    tests/test_apis/test_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_auth_reset_token.py
	renamed:    tests/test_apis/test_api_authentication/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/testi_auth_remove.py
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	new file:   tests/test_apis/test_api_prefix/__init__.py
	renamed:    tests/test_apis/test_prefixes_create.py -> tests/test_apis/test_api_prefix/test_prefixes_create.py
	renamed:    tests/test_apis/test_prefixes_modify.py -> tests/test_apis/test_api_prefix/test_prefixes_modify.py
	deleted:    tests/test_apis/test_auth_remove.py
	new file:   tests/test_apis/test_biocompute/__init__.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/test_objects_drafts_create.py
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   prefix/services.py
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   config/urls.py
Changes to be committed:
	modified:   config/fixtures/local_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	deleted:    tests/test_apis/test_auth_add.py
	deleted:    tests/test_apis/test_auth_remove.py
	deleted:    tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_prefixes_create.py
	deleted:    tests/test_apis/test_prefixes_modify.py
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   prefix/selectors.py
	deleted:    tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_biocompute/test_objects_drafts_create.py
HadleyKing and others added 27 commits April 11, 2024 12:06
* Add DraftsModifyApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   prefix/selectors.py
	deleted:    tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Add IEEE schema
Changes to be committed:
	new file:   .secrets
	new file:   config/IEEE/2791object.json
	new file:   config/IEEE/description_domain.json
	new file:   config/IEEE/error_domain.json
	new file:   config/IEEE/execution_domain.json
	new file:   config/IEEE/io_domain.json
	new file:   config/IEEE/parametric_domain.json
	new file:   config/IEEE/provenance_domain.json
	new file:   config/IEEE/usability_domain.json

* test_objects_drafts_create
Changes to be committed:
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Fix test
Changes to be committed:
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Enable publish bco endpoint

This included a great many supporting functions
and permission checks to accomplish. Also added
the validate functions to the codebase

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/services.py
	modified:   docs/refactor.md
	modified:   prefix/selectors.py
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py
Also added functions and methods for BCO Score.
Updates to the BCO admin panel.
Updates to the `test_data.json` and `local_data.json`
Fix # 310
Changes to be committed:
	modified:   authentication/migrations/0001_initial.py
	modified:   biocompute/admin.py
	modified:   biocompute/apis.py
	modified:   biocompute/migrations/0001_initial.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	new file:   config/bco_scores.py
	modified:   config/fixtures/local_data.json
	modified:   tests/fixtures/test_data.json
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   search/apis.py
	modified:   search/selectors.py
	modified:   search/urls.py
Changes to be committed:
	modified:   authentication/apis.py
	modified:   search/apis.py
also updated accounts/describe
Changes to be committed:
	modified:   .gitignore
	new file:   .secrets.example
	modified:   authentication/selectors.py
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   config/settings.py
	deleted:    server.conf
	deleted:    sever.conf.example
Changes to be committed:
	deleted:    .secrets
	modified:   config/settings.py
	modified:   config/urls.py
Changes to be committed:
	modified:   config/services.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py
* Created test_objects_drafts_modify, hasn't passed test yet

* Created test_objects_drafts_modify, hasn't passed test yet

* Created test_objects_drafts_modify, hasn't passed test yet

* new tests

* Update modify_prefix permissions
Changes to be committed:
	modified:   authentication/selectors.py
	modified:   config/fixtures/local_data.json
	modified:   prefix/services.py

* Created and tested test_objects_drafts_modify API

* Fixes for Prefix creation

Changes to be committed:
	modified:   config/services.py
	modified:   prefix/apis.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py

* Add UserSearch endpoint

Changes to be committed:
	modified:   prefix/apis.py
	modified:   prefix/selectors.py
	modified:   search/apis.py
	modified:   search/urls.py

* Fixes for deployment

 Changes to be committed:
	modified:   .secrets.example
	modified:   admin_only/bco_api.service
	modified:   biocompute/apis.py
	modified:   config/fixtures/test_portal.json
	modified:   config/settings.py
	modified:   tests/fixtures/test_data.json
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* test_objects_drafts_publish failed. Kicking back to Hadley for more investigation

* Update bco_api.conf

Changes to be committed:
	modified:   admin_only/bco_api.conf

---------

Co-authored-by: tianywan819 <[email protected]>
Co-authored-by: acoleman29 <[email protected]>
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/bco_scores.py
	modified:   config/services.py
	modified:   config/settings.py
	modified:   config/urls.py
	modified:   tests/fixtures/test_data.json
	renamed:    tests/fixtures/example_bco.py -> tests/fixtures/testing_bcos.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_modify.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/urls.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py
Changes to be committed:
	modified:   config/services.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/apis.py
Changes to be committed:
	modified:   biocompute/apis.py
Changes to be committed:
	modified:   config/fixtures/test_portal.json
Changes to be committed:
	modified:   admin_only/bco_api.conf
	modified:   config/fixtures/test_portal.json
Changes to be committed:
	modified:   config/services.py
Changes to be committed:
	modified:   biocompute/services.py
	modified:   config/services.py
Changes to be committed:
	modified:   biocompute/apis.py
Changes to be committed:
	modified:   authentication/apis.py
	modified:   authentication/services.py
	modified:   search/apis.py
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   search/apis.py
	modified:   tests/fixtures/testing_bcos.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py
Changes to be committed:
	modified:   authentication/apis.py
	modified:   authentication/services.py
	modified:   authentication/urls.py
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/urls.py
	modified:   prefix/services.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py
Changes to be committed:
	modified:   prefix/apis.py
On branch docs
Your branch is up to date with 'origin/docs'.
@HadleyKing HadleyKing merged commit 2c4e0d2 into 24.04 May 20, 2024
0 of 2 checks passed
HadleyKing added a commit that referenced this pull request May 20, 2024
* Change `bcodb` directory to `config` directory

Changes to be committed:
	modified:   .gitignore
	deleted:    bcodb/settings.py
	renamed:    bcodb/__init__.py -> config/__init__.py
	renamed:    bcodb/asgi.py -> config/asgi.py
	renamed:    bcodb/fixtures/local_data.json -> config/fixtures/local_data.json
	renamed:    bcodb/fixtures/test_portal.json -> config/fixtures/test_portal.json
	renamed:    bcodb/urls.py -> config/urls.py
	renamed:    bcodb/wsgi.py -> config/wsgi.py
	modified:   manage.py

* Create NewUser model and remove new_user model

changed model behind `/api/accounts/new/`
Changes to be committed:
	modified:   api/admin.py
	new file:   api/migrations/0006_delete_new_users.py
	modified:   api/models.py
	deleted:    api/scripts/method_specific/POST_api_accounts_new.py
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/admin.py
	modified:   authentication/apis.py
	new file:   authentication/migrations/0002_newuser.py
	modified:   authentication/models.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   tests/fixtures/test_data.json
	modified:   tests/test_views/test_api_account_activate.py
	modified:   tests/test_views/test_api_account_new.py

* Add example values to test account request

Changes to be committed:
	modified:   authentication/apis.py
	new file:   docs/refactor.md

* Account activation has been enabled.

On branch account_authorization
Changes to be committed:
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/apis.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   authentication/urls.py

* Account authorization (#277)

* Account activation has been enabled.

On branch account_authorization
Changes to be committed:
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/apis.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   authentication/urls.py

* get_new_user

* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Swagger move (#283)

* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Move Swagger files and implement BCO draft create

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	new file:   config/services.py
	modified:   config/urls.py
	modified:   docs/refactor.md
	modified:   prefix/urls.py
	new file:   tests/fixtures/example_bco.py
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Doc fix in Bco.models
Changes to be committed:
	modified:   biocompute/models.py

* Biocompute model (#284)

* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Move Swagger files and implement BCO draft create

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	new file:   config/services.py
	modified:   config/urls.py
	modified:   docs/refactor.md
	modified:   prefix/urls.py
	new file:   tests/fixtures/example_bco.py
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Doc fix in Bco.models
Changes to be committed:
	modified:   biocompute/models.py

* Updated biocompute.model and prefix.model

Added the DraftsCreateApi and tests.
This included serializers for BCO creation
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/services.py
	modified:   prefix/models.py
	modified:   prefix/services.py
	modified:   test.json
	modified:   tests/fixtures/test_data.json
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Implemented PrefixesCreateApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/apis.py
	modified:   prefix/services.py
	modified:   prefix/urls.py
	modified:   search/apis.py
	modified:   tests/test_views/test_api_auth_remove.py
	modified:   tests/test_views/test_api_objects_drafts_create.py
	new file:   tests/test_views/test_api_prefixes_create.py

* Added Prefix management URLs and APIs

Changes to be committed:
	modified:   config/fixtures/local_data.json
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/services.py
	modified:   prefix/urls.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_views/test_api_prefixes_create.py
	new file:   tests/test_views/test_prefixes_create.py
	new file:   tests/test_views/test_prefixes_modify.py

* Cleaning up some things
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/migrations/0001_initial.py
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	new file:   tests/test_views/test_account_activate.py
	new file:   tests/test_views/test_account_describe.py
	new file:   tests/test_views/test_account_new.py
	new file:   tests/test_views/test_auth_add.py
	new file:   tests/test_views/test_auth_remove.py
	new file:   tests/test_views/test_auth_reset_token.py
	new file:   tests/test_views/test_objects_drafts_create.py

* Add prefix creation function
Changes to be committed:
	modified:   authentication/services.py
	modified:   biocompute/models.py
	modified:   config/settings.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/models.py
	modified:   prefix/services.py
	modified:   tests/test_views/test_api_objects_drafts_create.py

* Add Prefix Modify API endpoint
On branch prefix_perms
Your branch is up to date with 'origin/prefix_perms'.

Changes to be committed:
	modified:   config/services.py
	modified:   prefix/apis.py
	modified:   prefix/models.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py

* response_c

* Add `DraftRetrieveApi`

To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json

* Update testing functions

Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py

* Add `DraftRetrieveApi`

To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json

* Update testing functions

Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py

* Update to Test functions

Changes to be committed:
	modified:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	modified:   prefix/services.py
	new file:   tests/fixtures/bco_dump.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_add.py
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_apis/test_auth_add.py -> tests/test_apis/test_api_authentication/test_auth_add.py
	renamed:    tests/test_apis/test_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_auth_reset_token.py
	renamed:    tests/test_apis/test_api_authentication/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/testi_auth_remove.py
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	new file:   tests/test_apis/test_api_prefix/__init__.py
	renamed:    tests/test_apis/test_prefixes_create.py -> tests/test_apis/test_api_prefix/test_prefixes_create.py
	renamed:    tests/test_apis/test_prefixes_modify.py -> tests/test_apis/test_api_prefix/test_prefixes_modify.py
	deleted:    tests/test_apis/test_auth_remove.py
	new file:   tests/test_apis/test_biocompute/__init__.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Bco perms (#293)

* Add `DraftRetrieveApi`

To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json

* Update testing functions

Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py

* Update to Test functions

Changes to be committed:
	modified:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	modified:   prefix/services.py
	new file:   tests/fixtures/bco_dump.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_add.py
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_apis/test_auth_add.py -> tests/test_apis/test_api_authentication/test_auth_add.py
	renamed:    tests/test_apis/test_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_auth_reset_token.py
	renamed:    tests/test_apis/test_api_authentication/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/testi_auth_remove.py
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	new file:   tests/test_apis/test_api_prefix/__init__.py
	renamed:    tests/test_apis/test_prefixes_create.py -> tests/test_apis/test_api_prefix/test_prefixes_create.py
	renamed:    tests/test_apis/test_prefixes_modify.py -> tests/test_apis/test_api_prefix/test_prefixes_modify.py
	deleted:    tests/test_apis/test_auth_remove.py
	new file:   tests/test_apis/test_biocompute/__init__.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Add `access_count` incrementer to DraftRetrieveApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   prefix/services.py

* Added PublishedRetrieveApi class
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   config/urls.py

* Update test DB and testing functions

Changes to be committed:
	modified:   config/fixtures/local_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	deleted:    tests/test_apis/test_auth_add.py
	deleted:    tests/test_apis/test_auth_remove.py
	deleted:    tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_prefixes_create.py
	deleted:    tests/test_apis/test_prefixes_modify.py

* Add DraftsModifyApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   prefix/selectors.py
	deleted:    tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_biocompute/test_objects_drafts_create.py

* test for objects_drafts_create

Changes to be committed:
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* split("/")

* Publish draft (#308)

* Add DraftsModifyApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   prefix/selectors.py
	deleted:    tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Add IEEE schema
Changes to be committed:
	new file:   .secrets
	new file:   config/IEEE/2791object.json
	new file:   config/IEEE/description_domain.json
	new file:   config/IEEE/error_domain.json
	new file:   config/IEEE/execution_domain.json
	new file:   config/IEEE/io_domain.json
	new file:   config/IEEE/parametric_domain.json
	new file:   config/IEEE/provenance_domain.json
	new file:   config/IEEE/usability_domain.json

* test_objects_drafts_create
Changes to be committed:
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Fix test
Changes to be committed:
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Enable publish bco endpoint

This included a great many supporting functions
and permission checks to accomplish. Also added
the validate functions to the codebase

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/services.py
	modified:   docs/refactor.md
	modified:   prefix/selectors.py
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* Add BCO Score to model.

Also added functions and methods for BCO Score.
Updates to the BCO admin panel.
Updates to the `test_data.json` and `local_data.json`
Fix # 310
Changes to be committed:
	modified:   authentication/migrations/0001_initial.py
	modified:   biocompute/admin.py
	modified:   biocompute/apis.py
	modified:   biocompute/migrations/0001_initial.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	new file:   config/bco_scores.py
	modified:   config/fixtures/local_data.json
	modified:   tests/fixtures/test_data.json

* Add BCODB search API endpoint.

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   search/apis.py
	modified:   search/selectors.py
	modified:   search/urls.py

* Add POST search
Changes to be committed:
	modified:   authentication/apis.py
	modified:   search/apis.py

* Updated config file to `.secrets`

also updated accounts/describe
Changes to be committed:
	modified:   .gitignore
	new file:   .secrets.example
	modified:   authentication/selectors.py
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   config/settings.py
	deleted:    server.conf
	deleted:    sever.conf.example

* Fix config/urls.py error
Changes to be committed:
	deleted:    .secrets
	modified:   config/settings.py
	modified:   config/urls.py

* Refactor `config/services.py::response_constructor`
Changes to be committed:
	modified:   config/services.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py

* Prefix registry (#318)

* Created test_objects_drafts_modify, hasn't passed test yet

* Created test_objects_drafts_modify, hasn't passed test yet

* Created test_objects_drafts_modify, hasn't passed test yet

* new tests

* Update modify_prefix permissions
Changes to be committed:
	modified:   authentication/selectors.py
	modified:   config/fixtures/local_data.json
	modified:   prefix/services.py

* Created and tested test_objects_drafts_modify API

* Fixes for Prefix creation

Changes to be committed:
	modified:   config/services.py
	modified:   prefix/apis.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py

* Add UserSearch endpoint

Changes to be committed:
	modified:   prefix/apis.py
	modified:   prefix/selectors.py
	modified:   search/apis.py
	modified:   search/urls.py

* Fixes for deployment

 Changes to be committed:
	modified:   .secrets.example
	modified:   admin_only/bco_api.service
	modified:   biocompute/apis.py
	modified:   config/fixtures/test_portal.json
	modified:   config/settings.py
	modified:   tests/fixtures/test_data.json
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* test_objects_drafts_publish failed. Kicking back to Hadley for more investigation

* Update bco_api.conf

Changes to be committed:
	modified:   admin_only/bco_api.conf

---------

Co-authored-by: tianywan819 <[email protected]>
Co-authored-by: acoleman29 <[email protected]>

* Fixes for testing files

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/bco_scores.py
	modified:   config/services.py
	modified:   config/settings.py
	modified:   config/urls.py
	modified:   tests/fixtures/test_data.json
	renamed:    tests/fixtures/example_bco.py -> tests/fixtures/testing_bcos.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_modify.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* "derrived_from": []

* fix test

* Add Validate url endpoint

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/urls.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* Update create test to include HOSTNAME

Changes to be committed:
	modified:   config/services.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Rollback status for validation

Changes to be committed:
	modified:   biocompute/apis.py

* Changes to be committed:
	modified:   biocompute/apis.py

* Typo fix
Changes to be committed:
	modified:   biocompute/apis.py

* Add `test_portal.json` for testing

Changes to be committed:
	modified:   config/fixtures/test_portal.json

* Testing fixes

Changes to be committed:
	modified:   admin_only/bco_api.conf
	modified:   config/fixtures/test_portal.json

* Fix for draft publish

Changes to be committed:
	modified:   config/services.py

* Add new_bco_instance.save()

Changes to be committed:
	modified:   biocompute/services.py
	modified:   config/services.py

* CustomJSONWebTokenAuthentication for GET Pub BCO
Changes to be committed:
	modified:   biocompute/apis.py

* Updates to authentication.apis.py
Changes to be committed:
	modified:   authentication/apis.py
	modified:   authentication/services.py
	modified:   search/apis.py

* Updates to biocompute.apis.py

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   search/apis.py
	modified:   tests/fixtures/testing_bcos.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Remove print statements

Changes to be committed:
	modified:   authentication/apis.py
	modified:   authentication/services.py
	modified:   authentication/urls.py
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/urls.py
	modified:   prefix/services.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* Updates to prefix.apis

Changes to be committed:
	modified:   prefix/apis.py

* print(

* change publish bco rejected response

On branch docs
Your branch is up to date with 'origin/docs'.

---------

Co-authored-by: tianywan819 <[email protected]>
Co-authored-by: acoleman29 <[email protected]>
@HadleyKing HadleyKing deleted the model_refactor branch May 20, 2024 14:57
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